PRS Residual Analysis - White and Black REGARDS Subjects
Jack Pattee
11/9/2023
This report documents unsupervised learning analyses of the model residuals for traits measured in white and black REGARDS subjects (documented in the ‘baseline.csv’ file downloaded from Suraju Sadeeq’s OneDrive). The following outcomes will be considered for inclusion as traits:
eGFR, documented as ‘EGFR_CKDEPI’, left ventricular hypertrophy: ‘lvh_main’, atrial fibrillation: ‘Afib_SR_ECG’, diabetes: ‘Diab_SRMed_glu’, lipidemia: ‘lipidemia_meds_labs’, myocardial infarction: ‘MI_SR_ECG’, CAD: ‘CAD_SR_ECG’, insulin, creatinine level: ‘Creatinine_urine’, albumin level: ‘Albumin_urine’, cystatin C level: ‘Cysc’, C-reactive protein: ‘Crp’, triglycerides: ‘Trigly’, glucose, LDL, HDL, DBP, SBP, cholesterol: ‘Cholest’, heart rate: ‘Heartrate’, stroke: ‘Stroke_SR’, depression (as scale): ‘CESD’.
Some variables are excluded based on inspection. CESD is highly skewed and does not appear to cohere to the Center for Epidemiological Studies - Depression scale, so it will be dropped. In this case, no subject has CESD>12, whereas the CES-D scale ranges from 0 to 60, and individuals are considered at risk for depression when the score exceeds 16.
Report the missing rate for each outcome Only one variable has missing rate >5%, which is insulin. Insulin will be dropped from consideration.
| Outcome | MissingProp |
|---|---|
| EGFR_CKDEPI | 0.025 |
| lvh_main | 0.015 |
| Diab_SRMed_glu | 0.025 |
| Lipidemia_meds_labs | 0.027 |
| Afib_SR_ECG | 0.024 |
| MI_SR_ECG | 0.018 |
| CAD_SR_ECG | 0.019 |
| insulin | 0.268 |
| Creatinine_urine | 0.047 |
| Albumin_urine | 0.049 |
| DBP | 0.003 |
| SBP | 0.003 |
| Cysc | 0.043 |
| Crp | 0.042 |
| Trigly | 0.026 |
| Glucose | 0.025 |
| Ldl | 0.041 |
| Hdl | 0.032 |
| Cholest | 0.025 |
| Heartrate | 0.012 |
| Stroke_SR | 0.003 |
The following variables will be considered as covariates in the analysis: alcohol use ‘Alc_Use’, gender ‘Gender_x’, age ‘Age_x’, smoking ‘Smoke’, education ‘ED_Cat’, income ‘Income’, weight ‘Weight’, and race ‘Race_x’.
Report the missing rate for each covariate. Income is the only covariate missing at >5%; it will be dropped, and the other seven retained. A complete case analysis will be performed on all individuals non-missing for both the covariates and the outcomes.
| Covariate | MissingProp |
|---|---|
| Weight | 0.000 |
| Smoke | 0.004 |
| Alc_Use | 0.000 |
| ED_Cat | 0.001 |
| Income | 0.123 |
| Gender_x | 0.000 |
| Race_x | 0.000 |
| Age_x | 0.000 |
The complete case analysis consists of 9290 subjects.
The following outcomes are binary (and thus, logistic regression will be used): LVH, Diabetes, Lipidemia, MI, CAD, Stroke. The frequency of the less common category for these binary outcomes is described below.
| Outcome | RareProp |
|---|---|
| lvh_main | 0.134 |
| Diab_SRMed_glu | 0.269 |
| Lipidemia_meds_labs | 0.448 |
| Afib_SR_ECG | 0.078 |
| MI_SR_ECG | 0.109 |
| CAD_SR_ECG | 0.147 |
| Stroke_SR | 0.060 |
Calculate the coefficient of determination for each of the models to give a sense of how predictive each covariate is. For the logistic models, use AUROC. These plots are interpreted as follows: the point label represents the predictive accuracy of the model without that variable included.
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Assess clustering and PCs for full set of residuals.
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
Assess clustering and PCs for model residuals with each of the seven covariates held out.
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## [1] "Adjusted rand index, no Alcohol: 0.023"
## [1] "No Alcohol table of clustering results"
## tempCovarValues
## Current Never Past
## 1 2935 1887 1216
## 2 794 790 567
## 3 437 355 309## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations
## [1] "Adjusted rand index, no Gender: 0.013"
## [1] "No Gender table of clustering results"
## tempCovarValues
## F M
## 1 593 636
## 2 4738 3323## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## [1] "Adjusted rand index, no Smoking: 0.007"
## [1] "No Smoking table of clustering results"
## tempCovarValues
## Current Never Past
## 1 1027 2825 2177
## 2 351 935 879
## 3 220 414 462## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## [1] "Adjusted rand index, no Education: 0.008"
## [1] "No Education table of clustering results"
## tempCovarValues
## College graduate and above High school graduate Less than high school
## 1 1345 1072 564
## 2 627 614 314
## 3 445 519 417
## 4 296 280 210
## tempCovarValues
## Some college
## 1 1182
## 2 618
## 3 513
## 4 274## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## [1] "Adjusted rand index, no Race: 0.042"
## [1] "No Race table of clustering results"
## tempCovarValues
## B W
## 1 6781 1271
## 2 957 281